def normalize_mc_params(params, source):
"""
Normalize a single row of motion parameters to the SPM format.
SPM saves motion parameters as:
x Right-Left (mm)
y Anterior-Posterior (mm)
z Superior-Inferior (mm)
rx Pitch (rad)
ry Roll (rad)
rz Yaw (rad)
"""
if source.upper() == 'FSL':
params = params[[3, 4, 5, 0, 1, 2]]
elif source.upper() in ('AFNI', 'FSFAST'):
params = params[np.asarray([4, 5, 3, 1, 2, 0]) + (len(params) > 6)]
params[3:] = params[3:] * np.pi / 180.
elif source.upper() == 'NIPY':
from nipy.algorithms.registration import to_matrix44, aff2euler
matrix = to_matrix44(params)
params = np.zeros(6)
params[:3] = matrix[:3, 3]
params[-1:2:-1] = aff2euler(matrix)
return params
def _get_affine_matrix(params, source):
"""Return affine matrix given a set of translation and rotation parameters
params : np.array (upto 12 long) in native package format
source : the package that generated the parameters
supports SPM, AFNI, FSFAST, FSL, NIPY
"""
if source == 'FSL':
params = params[[3, 4, 5, 0, 1, 2]]
elif source in ('AFNI', 'FSFAST'):
params = params[np.asarray([4, 5, 3, 1, 2, 0]) + (len(params) > 6)]
params[3:] = params[3:] * np.pi / 180.
if source == 'NIPY':
# nipy does not store typical euler angles, use nipy to convert
from nipy.algorithms.registration import to_matrix44
return to_matrix44(params)
# process for FSL, SPM, AFNI and FSFAST
rotfunc = lambda x: np.array([[np.cos(x), np.sin(x)],
[-np.sin(x), np.cos(x)]])
q = np.array([0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0])
if len(params) < 12:
params = np.hstack((params, q[len(params):]))
params.shape = (len(params),)
# Translation
T = np.eye(4)
T[0:3, -1] = params[0:3]
# Rotation
Rx = np.eye(4)
Rx[1:3, 1:3] = rotfunc(params[3])
Ry = np.eye(4)
Ry[(0, 0, 2, 2), (0, 2, 0, 2)] = rotfunc(params[4]).ravel()
Rz = np.eye(4)
Rz[0:2, 0:2] = rotfunc(params[5])
# Scaling
S = np.eye(4)
S[0:3, 0:3] = np.diag(params[6:9])
# Shear
Sh = np.eye(4)
Sh[(0, 0, 1), (1, 2, 2)] = params[9:12]
if source in ('AFNI', 'FSFAST'):
return np.dot(T, np.dot(Ry, np.dot(Rx, np.dot(Rz, np.dot(S, Sh)))))
return np.dot(T, np.dot(Rx, np.dot(Ry, np.dot(Rz, np.dot(S, Sh)))))
def _get_affine_matrix(params, source):
"""Return affine matrix given a set of translation and rotation parameters
params : np.array (upto 12 long) in native package format
source : the package that generated the parameters
supports SPM, AFNI, FSFAST, FSL, NIPY
"""
if source == 'FSL':
params = params[[3, 4, 5, 0, 1, 2]]
elif source in ('AFNI', 'FSFAST'):
params = params[np.asarray([4, 5, 3, 1, 2, 0]) + (len(params) > 6)]
params[3:] = params[3:] * np.pi / 180.
if source == 'NIPY':
# nipy does not store typical euler angles, use nipy to convert
from nipy.algorithms.registration import to_matrix44
return to_matrix44(params)
#process for FSL, SPM, AFNI and FSFAST
rotfunc = lambda x: np.array([[np.cos(x), np.sin(x)],
[-np.sin(x), np.cos(x)]])
q = np.array([0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0])
if len(params) < 12:
params = np.hstack((params, q[len(params):]))
params.shape = (len(params), )
# Translation
T = np.eye(4)
T[0:3, -1] = params[0:3]
# Rotation
Rx = np.eye(4)
Rx[1:3, 1:3] = rotfunc(params[3])
Ry = np.eye(4)
Ry[(0, 0, 2, 2), (0, 2, 0, 2)] = rotfunc(params[4]).ravel()
Rz = np.eye(4)
Rz[0:2, 0:2] = rotfunc(params[5])
# Scaling
S = np.eye(4)
S[0:3, 0:3] = np.diag(params[6:9])
# Shear
Sh = np.eye(4)
Sh[(0, 0, 1), (1, 2, 2)] = params[9:12]
if source in ('AFNI', 'FSFAST'):
return np.dot(T, np.dot(Ry, np.dot(Rx, np.dot(Rz, np.dot(S, Sh)))))
return np.dot(T, np.dot(Rx, np.dot(Ry, np.dot(Rz, np.dot(S, Sh)))))
